From a physics point of view, the emergence of a traffic jam is considered to be a dynamical phase transition. To verify this, we performed a series of circuit experiments. In previous work, Tadaki et al (2013 New J. Phys 15 103034), we confirmed ...

?-synuclein (?-syn) is an intrinsically disordered protein which is considered to be one of the causes of Parkinson’s disease. This protein forms amyloid fibrils when in a highly concentrated solution. The fibril formation of ?-syn is induced not ...

Proteins: Structure, Function, and Bioinformatics 83(5) 809-819 May 2015 [Refereed]

Molecular motors such as kinesin regulate affinity to a rail protein during the ATP hydrolysis cycle. The regulation mechanism, however, is yet to be determined. To understand this mechanism, we investigated the structural fluctuations of the moto...

How rare are magic squares? So far, the exact number of magic squares of order n is only known for n 5. For larger squares, we need statistical approaches for estimating the num- ber. For this purpose, we formulated the problem as a combinatorial ...

An intrinsically disordered protein (IDP) lacks a stable three-dimensional structure, while it folds into a specific structure when it binds to a target molecule. In some IDP-target complexes, not all target binding surfaces are exposed on the out...

The emergence of a traffic jam is considered to be a dynamical phase transition in a physics point of view; traffic flow becomes unstable and changes phase into a traffic jam when the car density exceeds a critical value. In order to verify this v...

Dynamics in biological networks are, in general, robust against several perturbations. We investigate a coupled map network as a model motivated by gene regulatory networks and design systems that are robust against phenotypic perturbations (pertu...

A group of barchans, crescent sand dunes, exhibit a characteristic flying-geese pattern in deserts on Earth and Mars. This pattern implies that an indirect interaction between barchans, mediated by an inter-dune sand stream, which is released from...

Katsuki, A., Kikuchi, M., Nishimori, H., Endo, N. and Taniguchi, K.

Earth Surface Processes and Landforms 36 372-382 Mar 2011 [Refereed]

Barchans are crescent-shaped dunes that form under unidirectional wind in areas of limited sand supply. The recent development of flume experiments and computer simulations has renewed interest in the interaction dynamics of two or more barchans. ...

Eureka in the Age of Science and Pseudoscience

Macoto Kikuchi

Journal of the Poe Society of Japan 1 61 Sep 2009 [Invited]

Proteins: Structure, Function, and Bioinformatics 71(1) 389-395 Apr 2008 [Refereed]

Structural fluctuations in the thermal equilibrium of the kinesin motor domain are studied using a lattice protein model with G? interactions. By means of the multi-self-overlap ensemble Monte Carlo method and the principal component analysis, the...

A traffic jam on a highway is a very familiar phenomenon. From the physical viewpoint, the system of vehicular flow is a non-equilibrium system of interacting particles (vehicles). The collective effect of the many-particle system induces the inst...

J. Phys. Soc. Jpn. 76(10) 103801 Oct 2007 [Refereed]

It is widely accepted that the folding process of a protein is in large part determined by topology of the native structure. A class of coarse-grained model called Go-like model that takes only the native-state topology into account has successful...

We investigated the structural relaxation of myosin motor domain from the pre-power stroke state to the near-rigor state using molecular dynamics simulation of a coarse-grained protein model. To describe the spontaneous structural change, we propo...

Chem. Phys. Lett. 427(4-6) 414-417 Aug 2006 [Refereed]

To elucidate the role of relative stability of subdomains in folding processes of multi-domain proteins, we have studied a free-energy landscape of c-type lysozyme by Monte Carlo simulations using a realistic lattice model with a G?-like interacti...

J. Phys. Soc. Jpn. 75(6) 64803 May 2006 [Refereed]

We investigate aggregation mechanism of two proteins in a thermodynamically unambiguous manner by considering the finite size effect of free energy landscape of HP lattice protein model. Multi-self-overlap-ensemble Monte Carlo method is used for n...

We observed the time evolution of dune fields in a water tank experiment and simulated it by using a simple model without taking complex fluid dynamics into account. The initial sand bed changed its form to transverse ripples, that is, dunes with ...

Long-Term Traffic Data from Japanese Expressway

M. Kikuchi, A. Nakayama, K. Nishinari, Y. Sugiyama, S. Tadaki and S. Yukawa

Traffic and Granular Flow '01 Apr 2003 [Refereed]

Observational Aspects of Japanese Highway Traffic

S. Yukawa, M. Kikuchi, A. Nakayama, K. Nishinari, Y. Sugiyama and S. Tadaki

Traffic and Granular Flow '01 Apr 2003 [Refereed]

Congestion Induced by Bottlenecks in Two-lane Optimal Velocity Traffic Flow Model

S. Tadaki, M. Kikuchi, K. Nishinari, Y. Sugiyama and S. Yukawa

As an introduction to the special topics section of traffic flow problem, a brief history of mathematical researches in this area is described. Some basic concepts, such as a q-k diagram, are introduced at the same time.

Proc. Natl. Acad. Sci. 97 (2000) 14273-14277. Apr 2000 [Refereed]

The mechanism of α→β transition in folding of β-lactoglobulin is discussed based on free energy landscape analysis of a long lattice model. It is found that helical propensity of β-lactoglobulin is driven by conformational entropy and is intrinsic...

Phys. Rev. Lett. 83(9) 1886-1889 Apr 1999 [Refereed]

Long chains of the HP lattice protein model are studied by the multi-self-overlap ensemble Monte Carlo method, which was developed recently by Iba, Chikenji, and Kikuchi. This method successfully finds the lowest energy states reported before for ...

Journal of Physical Society of Japan 67(11) 3985-3990 Nov 1998 [Refereed]

A novel approach to heteropolymer design is proposed. It is based on the criterion by Kurosky and Deutsch, with which the probability of a target conformation in a conformation space is maximized at low but finite temperature. The key feature of t...

J. Phys. Soc. Jpn. 67(10) 3327-3330 Apr 1998 [Refereed]

A novel family of dynamical Monte Carlo algorithms for lattice polymers is proposed. Our central idea is to simulate an extended ensemble in which the self-avoiding condition is systematically weakened. The degree of self-overlap is controlled in ...

J. Phys. Soc. Jpn. 67(7) 2270-2276 Apr 1998 [Refereed]

A coupled map traffic flow model is introduced, based on optimal velocity functions. The model is simulated under open boundary conditions. Effects of noises in velocity are investigated. The average car density increases with the noise level. The...

Coupled-Map Modeling of One-Dimensional Traffic Flow

J. Phys. Soc. Jpn. 67(4) 1090-1093 Apr 1998 [Refereed]

Quantum mechanical motion of a particle in a periodic asymmetric potential is studied theoretically at zero temperature. It is shown based on a semi-classical approximation that the tunneling probability from one local minimum to the next becomes ...

We apply a recently developed numerical renormalization group, the corner-transfer-matrix renormalization group (CTMRG), to 2D classical lattice models at their critical temperatures. It is shown that the combination of CTMRG and the finite-size s...

International J. Mod. Phys. C 6 747-763 Apr 1995 [Refereed]

The multi-spin coding of the Monte Carlo simulation of the three-state Potts model on the simple cubic lattice is presented. The ferromagnetic (F) model, the antiferromagnetic (AF) model, and the random mixture of the F and AF couplings are treate...

J. Phys. Soc. Jpn. 64(1) 35-38 Apr 1995 [Refereed]

We propose a new model of one-dimensional traffic flow using a coupled map lattice. In the model, each vehicle is assigned a map and changes its velocity according to it. A single map is designed so as to represent the motion of a vehicle properly...

Monte Carlo Studies of Phase Transitions in Polymer Blends and Block Copolymer Melts

K. Binder, H.-P. Deutsch, M. Mueller, H. Fried and M. Kikuchi

J. Phys. Soc. Jpn. 63(10) 3609-3618 Apr 1994 [Refereed]

Effects of a bottleneck in a linear trafficway is investigated using a simple cellular automaton model. Introducing a blockage site which transmit cars at some transmission probability into the rule-184 cellular automaton, we observe three differe...

Statistical Dependence and Related Topics

M. Kikuchi, N. Ito, and Y. Okabe

Computer Simulations in Condensed Matter Physics VII Apr 1994 [Refereed]

By means of Monte Carlo simulations of a lattice model, microphase separation transition of symmetric diblock‐copolymer melts confined in the thin‐film geometry between parallel hard walls is studied. We impose a surface field which acts repulsive...

J. Phys. Soc. Jpn. 62(9) 3052-3061 Apr 1993 [Refereed]

A new method for studying dynamical correlation of temporal sequence is proposed. We introduce a new quantity named statistical dependence time τ dep as an estimator for the equilibrium relaxation time. The calculation of τ dep does not require ca...

Recycle of Random Sequences

N. Ito, M. Kikuchi and Y. Okabe

International J. of Mod. Phys. C 4 569-590 Apr 1993 [Refereed]

A numerical method to study defect-mediated phase transitions is proposed, which combines a standard Monte Carlo technique with a particular type of boundary conditions. The method is applied to the two-dimensional XY (plane rotator) model as well...

Random three-state Potts model: a Monte Carlo study

Y. Okabe and M. Kikuchi

Computer Aided Innovation of New Materials II Apr 1993 [Refereed]

Application of Finite-Size Scaling to Phase Transitions and Localization-Delocalization Transitions

J. Phys. Soc. Jpn. 59(2) 492-496 Apr 1990 [Refereed]

We study the effect of anisotropy for the ground state of the spin 1/2 antiferromagnet on the square lattice by diagonalizing the Hamiltonian numerically. The symmetry change of the ground state at the isotropic point is discussed.

Numerical Studies of Two-Dimensional Quantum Spin Systems

Y. Okabe and M. Kikuchi

Quantum Simulations of Condensed Matter Phenomena Apr 1990 [Refereed]

J. Phys. Soc. Jpn. 57(12) 4351-4358 Apr 1988 [Refereed]

We systematically study the spin 1/2 quantum XXZ model on the square lattice using a quantum Monte Carlo method. The temperature dependence of the energy, specific heat and order parameter is calculated for the systems of sizes up to 16×16. Invest...

Growth Process of Order Parameter -- Block Spin Analysis --

M. Kikuchi and Y. Okabe

Dynamics of Ordering Processes in Condensed Matter Apr 1987 [Refereed]

We propose a simple method of Monte Carlo renormalization group. Thermodynamic quantities of the block-spin system are analyzed phenomenologically on the basis of scaling concept. The field exponent yH is obtained from the square of block-spin mag...

We present a new method for studying the temporal evolution of order-parameter structure. The relaxation of the block-spin magnetization ratio of the three-dimensional kinetic Ising model is investigated by use of a Monte Carlo simulation with a b...

High-Speed Algorithm for Quantum Monte Carlo Simulation

Y. Okabe and M. Kikuchi

Quantum Monte Carlo Methods in Equilibrium and Nonequilibrium Systems Apr 1987 [Refereed]

J. Phys. Soc. Jpn. 55 1359-1363 Apr 1986 [Refereed]

We report a Monte Carlo study on the critical relaxation of the three-dimensional kinetic Ising model from a nonequilibrium initial state. It is shown that the details of the method, namely, a choice of the sampling procedure and a functional form...

We report the first Monte Carlo simulation on the critical relaxation of the three-dimensional kinetic Ising model with free surfaces. The surface-layer magnetization is shown to relax as t^{?β1/νz} at T=Tc, while the bulk magnetization relaxes as...

Monte Carlo technique is applied to the three-dimensional Ising model with free surface. The critical behavior of the layer magnetization, the layer susceptibility and the local susceptibility near the ordinary transition point is investigated. Th...